rs7623146

Variant names:

• chr3-63718309-G-A
• rs7623146
• ENST00000829501.1:n.-236G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000829501.1(ENSG00000307865):​n.-236G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,080 control chromosomes in the GnomAD database, including 1,724 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1724 hom., cov: 32)
• Consequence: ENSG00000307865 ENST00000829501.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 1 publications found

Genes affected

ENSG00000307865 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829501.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307865	ENST00000829501.1		n.-236G>A		upstream_gene	N/A
	ENSG00000307865	ENST00000829502.1		n.-234G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22994 AN: 151962 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23024 AN: 152080 Hom.: 1724 Cov.: 32 AF XY: 0.152 AC XY: 11326 AN XY: 74358

African (AFR) AF: 0.128 AC: 5319 AN: 41502

American (AMR) AF: 0.177 AC: 2702 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1316 AN: 5168

South Asian (SAS) AF: 0.125 AC: 605 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1415 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10445 AN: 67986

Other (OTH) AF: 0.157 AC: 331 AN: 2110

Alfa AF: 0.145 Hom.: 216

Bravo AF: 0.158

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.26
PhyloP100		-0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7623146;

hg19: chr3-63703985;